Questions for Jonathan Eisen (Advice, Background, Projects, etc)

I am starting a new page here on my site for people who have general questions about our work or want advice on some issue like genomics, bioinformatics, microbial diversity etc. I get many many emails with such questions and have decided that I am only going to be able to answer them if they are posed publicly so others can see the answer.

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I have worked in a research lab for 4 years. I have lab skills (pcr, sequencing, cloning, cell culture, working with pathogens etc. ) but I lack a computer science background. I have started to learn python, but I am not sure if I am on the right track or the steps I need to take to get on the right track to apply for my masters in bioinformatics.

Any suggestions or guidelines on how to get some experience/ how to approach the switch from lab bio to computational bio would be very helpful!

I am an ulcerative colitis sufferer, fascinated by the possibility that it could be not the presence of pathogenic bacteria, but the absence of probiotic bacteria that causes the disease. I for one took six months of tetracycline around the time my symptoms started. I am interested in fecal transplants, but am treading carefully (I’m still curious to know what the neurological side effects would be).

Being curious about possible alternatives for repopulating digestive systems with missing bacteria, I was wondering what your thoughts are on the role of breast milk in the formation of an infant’s microbiome. One study found that breast milk promoted the formation of biofilms (http://www.dukehealth.org/health_library/news/breast-milk-promotes-a-different-gut-flora-growth-than-infant-formulas). Could it be that milk holds the key to repopulating gut flora? Perhaps there is something in raw bovine milk that could be isolated to encourage colonization of an ingested probiotic cocktail?

I actually came across a book published in the beginning of the last century that outlined a treatment endorsed by the mayo foundation at the time. The book is ‘The Milk Diet As A Cure For Chronic Disease’ by Charles Sanford Porter M.D. It advocates a thirty day all raw milk diet with bed rest. He claims that the diet works by promoting the development of blood, but given the conditions treated (constipation, ulcers of the stomach, eczema etc) could it be that it actually corrected dysbios. The doctor even claims “A gentlemen from Maine who suffered membranous colitis […] took the milk diet under my supervision and at the end of five weeks I discharged him permanently cured.”

I think vaginal delivery and breast feeding are partly a delivery system for microbes. So certainly human milk for the infant likely plays a massive role in colonization of the infant. There is in fact a large group here at UC Davis working on this. See http://ffhi.ucdavis.edu/prog/fg/proj/im . However, it is unclear if the same benefits would apply to adults .. part of what is going on in an infant is the immune system is developing and learning what is good vs. bad. What role milk would play in an adult is unclear.

Hope this email finds you well–apologies for spamming your blog. I am a new faculty member in the Department of Dermatology here at Stanford, and am interested in starting some translational work looking at bacterial and fungal microbiomes changes in some of our immunosuppressed patients–I have NGS experience with most of the molecular unfortunately do not have much experience with the specifics of microbiome genomics work–specifically, what the best methods are to make libraries from samples (looks like most of the literature that I can find are PCR-based with custom primers), and whether Illumina-based sequencing platforms are suitable for these types of projects. I am writing to see if you would have some interest in the project, and if not (I totally understand given the vast and varies projects you have ongoing!), we would still appreciate any guidance your lab can offer in setting up the data collection portion of the work up in our lab here.

Thank you very much in advance for your time and your help. I look forward to hearing from you.

Kevin … your comment got caught in a SPAM filter and I just found it and approved it. Very interested in talking about collaborating on this as we are doing work with people here on immunosuppressed patients too.

Just a couple of more questions, if I may? I’m having trouble finding what the specific change is to gut flora after it has been irreversibly affected by antibiotic treatment. Is it that biodiversity is lost (i.e. some species are eradicated), or is that a new homeostasis is reached (where all species remain, just in different numbers)?

Secondly, what books on the subject would you recommended for a laymen? All these journal articles are making my head dizzy!

There are not a lot of studies yet published to know conclusively what is going on with antibiotic treatment. But look for papers by David Relman and Martin Blaser and others. As for books for a layman … am thinking about writing one but there is not a lot out there. I would suggest blogs instead. Ed Yong and Carl Zimmer have some wonderful posts about the human microbiome from time to time. See http://blogs.discovermagazine.com/notrocketscience/category/microbiome-bacteria/#.URVNNKV8v8s for example.

I work in Rob Edwards’ Bioinformatics lab at SDSU as an undergrad. We are creating a microbial database based on phenotypic and biochemical microbial information, similar to what you would find in Bergey’s Manual of Determinative Bacteriology, or the information used in papers to classify microbes, such as metabolism, growth conditions, responses to various biochemical tests, etc. We are hoping to standardize the information we have collected and translate it into an ontology (for coding purposes) with the hopes of creating a open access website to publish and expand our database, with the option to submit new information on various microbes. The main idea is to eventually have an easily accessible and searchable database for microbes, not necessarily like MicrobeWiki, but more for facts and listed straight forward information for species/strain analysis and side-by-side comparison.

So far the most developed microbial ontology I have found is through the Microbial Phenotypes Wiki (http://microbialphenotypes.org/wiki/index.php/Category:OMP:0000000_!_microbial_phenotype), but unfortunately this ontology is limited as far as the biochemical tests are concerned (i.e., Lactose acid production, Citrate (Simmons) test, Phenylalanine deaminase (24h), etc.). Instead of simply creating our own ontology, we are hoping to find a standardized one and help collaborate on its growth.

Any help or suggestions you could provide would be appreciated. Also, do you know of any existing projects that sound similar to what we are doing?

do you have any experience with methods that enrich for microbial DNA vs. host/eukaryotic DNA? It appears there are a few commercial kits on the market, e.g. MolYsis from Molzym, Pureprove technology, but I can find no or few reports on their effectiveness or on possible introduction of bias on e.g. metagenomic 16S rRNA gene sequencing results.

We have some experience with this but nothing seems to work too well. The main experience involved projects to sequence genomes of endosymbionts and the methods involved ways to remove host cells and/or host cell materials. But they never worked so well in my hands.

My name is Larissa, I am a Brazilian graduate student and I have been working with helminth phylogenomics since 2008.

Over the last years, I have seen many scientists discussing about what is phylogenomics.

When you coined this term it was an intersection between phylogenetics and genomics to improve the prediction of gene/protein function.

However, over the last decade, the term “phylogenomics” has been used many times as synonym of phylogenetic analyses or to describe comparative analyses among entire genomes, or at least large portions of genomes, with many different aims:

-Prediction of gene function
-Establishment and clarification of evolutionary relationships
-Studies of parasite biology, among others.

Nowadays, what means phylogenomics to you? When you talk or write about phylogenomics do you keep the original definition or you believe that phylogenomics could be currently described as evolutionary comparative analyses of genome-scale data?

Apologies for the delay – was in Costa Rica on vacation. I think my 1st definition was too narrow and shortly thereafter I expanded the concept to refer to the general integration of phylogenetic and genomic studies. There are many aspects to this integration …

I am a PhD in the UK and I have just started to work with metagenomics. My samples are from a glacier in SE-Greenland and I will have whole shotgun metagenomic data (Illumina) soon. I am interested in the diversity and functional genes of prokaryotes AND eukaryotes. I am even more interested in eukaryotes because the glacial snow and ice fields are dominated by algae. Unfortunately most of the standard programs are only for prokaryotes. Do you know of a good program/pipeline which I could use for both?

I do not know of any tools / programs that specifically focus on eukaryotic metagenomics. But there are some things out there. For example in phylosift we are working to integrate marker genes for eukaryotes – see https://github.com/gjospin/PhyloSift/ to do phylogenetic diversity assessments. Holly Bik, who is a post doc in my lab – is probably one of the better people to ask about this. In fact, this AM I will be giving a talk in a special satellite SMBE meeting on “eukaryotic-omics” that Holly organized. This meeting will have a few talks on eukaryotic metagenomics. See http://www.genomecenter.ucdavis.edu/events/smbe-satellite-meeting-on-eukaryotic-omics for more information. People will be posting to Twitter notes from the meeting and I will post a summary here so maybe some useful tools will come up.

Jonathan,
Looking for a HOMEBREW microbiome DNA extraction protocol for samples with inhibitors compatible with 96-well plates and robotics BESIDES MoBio PowerSoil and similar kits (which work well but $). Jeff Gordon’s gut microbiome lab uses phenol/chloroform but their robot is outfitted with special ventilation pipes. Been searching recent pubs but it’s getting tiring. I follow you on Twitter and thought maybe I could leverage that to ask a quick question… I know you are very well connected. 🙂 Any leads ideas?
Derek S. Lundberg

Ended up doing basic SDS lysis with 1mm garnet rocks from Biospec, followed by simple SPRI bead cleanup on the crude lysate (homemade SPRI beads N Rohland et al. ‎2012, 40x cheaper than Ampure XP). For plant microbiome samples, better yield than Powersoil, much cheaper than PowerSoil or Qiagen, great quality DNA, and more control of reagents and batch effects. Has some problems with some soils though, so the PowerSoil chemistry still best solution for some of that stuff.

Hello I am interested to know if you know much about EM- effective micro-organisms http://www.emrojapan.com/about-em.html
and what your opinions on these products are in regards to how effective they are at maintaining full healthy micro organism cultures in our bodies.

I saw you published an Illumina sequenced genome of Candidatus Ruthia magnifica. I am investigating the microheterogeneity in the sulfur oxidizing symbionts of Bathymodiolus mussels which are, in contrast to Ruthia magnifica, horizontally transmitted. I’d like to compare my data to R. magnifica but for my analysis I need the raw reads of the sequencing project. Is there any chance you could provide me with these?

As I noted in the description, these are the reads that we believe belong to Ruthia based on mapping them to the Ruthia contigs from the original co-assembly (which was mostly host DNA). Let me know if this isn’t what you need.

Hello, I am a high school student who has been an avid reader in antibiotic resistance in preparation for this year’s science fair. I have been looking for feedback on a project idea and recently I have learned about a nonpathogenic bacteria Streptomyces platensis strain that produces two antibiotics at once- platensimycin and platencin, which helped the bacteria compete against other bacteria. A research team has discovered recently that there are two certain genes- ptmP3 and ptnP3, that are responsible for the streptomyces’s resistance to both its antibiotics. When these two genes are placed in other streptomyces species, such as streptomyces albus, that bacteria also showed resistance to the antibiotics. Knowing the genes responsible for resistance is very significant in the field of antibiotic resistance, but I can’t think of a way to follow up on this experiment with my own project. Any ideas or pieces of advice? Thank you!

Hi Ray, I’m a postdoc studying antibiotic resistance with Roy Kishony at Harvard Medical. Yes! Discovering resistance genes is important, especially when they are associated with production — Streptomyces often produce a large number of antibiotics simultaneously and we rarely can isolate and study more than a few at a time. I see two major directions you could go with this:

1) You could study just how important the resistance genes are. When you put them in other organisms, say, e. coli, staph, or bacillus, do they also confer resistance to platencin and platensimycin? But more importantly, if they do, how do they affect resistance to other drugs, especially common ones like ciprofloxacin, doxycycline, and erythromycin. Genes that give resistance to a single drug are certainly interesting, but they become far more clinically important when they also give resistance to commonly used drugs (because then there’s real selective pressure for them to spread in the clinic or on a farm).

2) You could try to study production. This is more open-ended and therefore more difficult, but you could try to figure out under what conditions you can encourage the platensis to produce more or less antibiotic. There are some pretty counterintuitive things that have been seen here, like streptos producing certain antibiotics only when nutrient starved.

I’m not sure what the lab capabilities you have access to are, so both of these might be difficult, but I’ve been impressed by the sophistication of high school projects before.

Thanks for the advice! My lab capabilities lack such equipment to isolate and study genes, so after doing a lot of reading and talking to other professors and school teachers, I found that bisphosphonates, drugs normally for osteoporosis, can inhibit conjugation of the F plasmid. As I thought more about this, I came across an idea of utilizing this conjugation inhibition in combination with competitor bacteria to render an infection harmless. In other words, I plan on engaging two nonpathogenic e. coli populations in vitro on the same plate (one e. coli k12 population having plasmids for ampicillin resistance and bioluminescence and the other being wild-type dh5 alpha) and using a bisphosphonate such as clodronic acid to inhibit conjugation of the resistance plasmid in combination with ampicillin to select for resistant bacteria. The use of the competitor bacteria and the bisphosphonate is to prevent/ slow the propagation of antibiotic resistance (AR) in the opposing wild-type population. By taking a sample of each the of the remaining bacteria populations after killing many wild-type dh5 alpha with bacterial competition and ampicillin, placing the samples in separate mediums for repopulation, and repeating the process until their population sizes reach an equilibrium and comparing this to a control test where unadjusted k12 and dh5 alpha compete under the selection of ampicillin, I can statistically find out whether utilizing this novel way of preventing AR can slow or prevent AR.

Ideally, I imagine that one day this novel approach can be used on actual infections by using a solution of antibiotic resistant nonpathogenic bacteria with bisphosphonate and antibiotic to not only destroy the pathogenic bacteria in an infection, but also prevent the growth and spread of antibiotic resistance genes in the surviving pathogenic bacteria through domination of the new nonpathogenic bacteria. Yet, there are two problems that I noticed with the applicability of this novel method:

1) Possibility of the pathoadaptation of nonpathogenic bacteria due to susceptibility to the immune system, which could lead to a new problem.

We have been doing desk research and field research for the last two weeks.Through diaries and questions given to general public and those close. It seems that peoples diet and mood is effected mostly around mid day. From what we can see people’s lunch could be the worst part of their diet. Our diaries showed that this happens due to stress and tiredness. We looked into these results and found there is new research to show that people with high fat or high sugar diet combined with disorganised Circadian sleep pattern effects there intestinal bacteria. The results can lead to inflammation and in turn results in wide variety of problems such as heart disease and diabetes.
I was hoping you could comment on our discoveries or tell us about some other avenues of research we could go down. Any other designers/projects you could suggest that are relevant to our topic?

Hi.. I’m a high school student..I’m an associate in a scientific competitions .. And I need your help please to complete the project..
I have a question about chromosomes and genetics
1- can I remove the chromosome for ever ??if the answer yes .. Tell my how ?!
2- what is the gene which can remove or bombing or decompose the chromosome ??
3- do you know any one can be my supervisor for my genetics research ??
If you can I want the answer too fast to complete my research !!
Finally .. Thanks 😢

I have a two year old daughter with severe eczema. The biggest challenge of eczema is staphloccus aureous. During flares a study showed that staph increases and biodiversity of the skin decreases. Most eczema treatment revolves around anti microbial washes that probably reduce good bacteria also. The staph always wins through.
My question is this. What is the best way to try to improve the colonies of good bacteria on my daughters skin in order to stop the dominance if staph. For instance would regular skin to skin contact with a healthy host transfer enough good bacteria to improve her skin biodiversity.

With regrets, I just don’t know anything about skin microbiomes and how to try to improve them. But in general it seems like a good idea to think about therpaies that do not just kill all the microbes on the skin. Every year or so there are papers on oral probiotics as a possible treatment for excema (or a preventative therapy). See for example http://www.reuters.com/article/2012/12/19/us-probiotics-skin-problems-idUSBRE8BI15H20121219. I just do not know the latest on this.

As for skin skin contact in theory that might help but I am just not sure. When flares happen, the higher levesl of Staph could be the cause of the flares or they could be the result of something that caused the flares.

So – in the end – I just don’t know. I may post to Twitter to ask anyone else if they know about this.

Thanks for replying Johnathon. I have read the Cochrane reviews on probiotics and while there is evidence that they can reduce the risk of developing eczema they can do little to treat it once it is established. Research into topical probiotics seems to be in its infancy. Gueniche et al 2008 is all I can find but L’oreal played a big part in this study so there is some conflict of interest. However Tubingen University (Volz et al) followed this up with some promising results in 2014 with Nonpathogenic Bacteria Alleviating Atopic Dermatitis Inflammation Induce IL-10-Producing Dendritic Cells and Regulatory Tr1 Cells.
Some probiotic creams are appearing on the market but the marketing bull makes it a minefield.(They are mainly aimed at anti-ageing).
So if any of your twitter followers could give me advice I would be very grateful.
Incidentally, the day my daughter was born she was whisked away from us and given antibiotics. I suspect that this played a part in both her eczema and food allergies.

Hi Dr Eisen
I’ve been reading/reviewing papers about transgenic crops. Several feeding studies have been carried out where animals are fed diets comprised of a transgenic crop or its control, and the impact on intestinal bacterial populations is determined through 16s rRNA sequencing (example: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370545/). The number of animals used in the studies are not consistent, so I was wondering how the proper calculation for the sample size should be done when examining the difference in microbiomes between two groups. Is the whole microbiome considered a single variable or is each bacterial strain a variable? I’d very much appreciate any guidance you could offer, or point me to a paper/book that may have the information. Thanks in advance.

I am high school student currently creating a website to enter into the annual Teen Biotech Challenge. Since, my website revolves around antimicrobial resistance, I would love your input on a few issues, mainly regarding the threat of drug resistance. I have a few brief questions below, but please include anything else you deem necessary.
1. Do you believe that antimicrobial resistance is a threat to global safety?
2. Should the average person be concerned resistance?
3. How should the average person combat resistance?
4. What should we, as a society, do to combat resistance?
I have also been researching phage therapy and I would love to hear your opinion on whether or not bacteriophages could be a viable solution to antimicrobial resistance.

So far, the topic is quite fascinating and it would be great if you could recommend articles for me to read or related topics to further research. Please reply to me if you can. Any help is greatly appreciated. Thank you in advance.

Dr. Eisen,
I am a 64 year old female with a developing complicated medical history beginning with 23+ of mild to moderate UC, which, at the moment is in remission. Last, April, I had a colonoscopy that resulted in aspirational pneumonia….an overnight hospital stay and a round of clyndamyicin, and, bingo, a recurrent c.diff infection resulting, finally, with a FMT at Mayo Clinic, October 6th, 2014. It has been a long year…
Since, then I have been diagnosed with post infectious IBS…… I already knew that. Trying all the diets…. considering naturopathic help, but, now I seem to be developing liver issues. Will make another call to the gastroenterologist tomorrow about that. I, also, have lichen sclerosis and have been treating it with clobetasol for at least a year and would very much like to taper off, but, when I try to it flares. My question for you is, is there any research indicating whether/what microbes play a part in this condition (lichen sclerosis) and is there anything I can do ? Also, would there be any point is seeing an immunologist, as well ?
I am so encouraged by what I read about the research regarding the human microbiome and potential treatments for so many diseases, but, for those of us waiting in the wings with these health issues it is a trying, frustrating time, I feel like I am falling down a well.
Thankyou,
Jeanne……. follower of the FMT Support group.

Alas I literally know nothing about lichen sclerosus (I am much more on the basic science side of things than the clinical side of things). I searched around and could not find anything about a microbiome connection to it. I am not saying there is no such connection – just that I could not find any literature on it.

Jonathan,
I recently came across some of your work and Ted Talk regarding microbiomes and there affect on our health. Over the past two years I have been struggling with multiple issues but mainly severe allergies to many substances including mold, dust, NSAIDs, numerous chemicals…and the list seems to keep growing. The allergies have greatly affected my quality of life and health. After multiple different approaches, all that failed, I began taking probiotics 3 days ago after some reading on the subject. For the first time in 2 years I had a full night of sleep, I am off antihistamines – and I feel much better. when I was younger, I took antibiotics for acne for multiple years. I also took some for strep throat about 2 1/2 years ago.
It seems now looking back that ever since I took the antibiotics I have had many issues, beginning with allergies. But I also had psoriasis/dry skin, minor stomach problems, and acne. All of these have been associated with antibiotic use b
Well to make a long story short…. My question is do you recommend a specific probiotic? And for how long to properly establish normal gut microbiomes? I know you mentioned in your Ted Talk that a single strain probably isn’t enough. Is it appropriate to take multiple probiotics to improve the amount a good bacteria in the stomac? Any recommendations you believe to help would be greatly appreciated.
Thanks
Greg

I note – human probiotics are not really my area of expertise. So … I am not really the person to ask. I personally have gone on antibiotics way way way more often than I would like (am on them right now …). I do not take a probiotic in response to these assaults on my system but I do try to get all sorts of microbes colonizing me via fermented foods like yogurt, kefir, and whatever else I can tolerate.

Jonathan,
Hello, my name is Jesse. I’m currently living in Fort Collins Colorado, age 22. I was recently listening to you in a podcast hosted by Tim Ferris. I was very interested in your work. I have no credentials in any fields of science but would love to get involved, if possible, in some type of field research. Whether its collecting samples of fecal matter or taking blood samples or whatever is possible for a man with my lack of knowledge. Is there any type of outreach community I could get involved with to further help your research.
How does one get involved with the research you are leading, or any type of microbial research and recording?

It is said that the average American has lost 40% of the diversity of the human microbiome, as compared to remote tribes that have never had antibiotics. We are also learning that damage to this ecosystem of bacteria, the human microbiome, is being associated with one disease after another. Since a one week course of antibiotics kill up to a third of the species, with some coming back after a year, and some that never do……….. it seems that we have an important need to 1. educate all health care professionals as to what the Human Microbiome is, 2. the huge role it plays in our health, and 3. how our over-use of antibiotics is doing more harm than good, and that we need to curb our use of antibiotics, whenever it is reasonable to do so. Please Sir, would you help to accomplish these goals in 2017 ? Will you encourage the NIH to accomplish this please ?

We also need to get the antibacterials out of the 700 products they are now in, that are available to consumers. The September, 2016 ruling by the FDA fell far short of stopping unnecessary exposure to antibiotics. The ban of antibacterials in hand soaps was a start, but we have a long way to go. Please Sir, would you encourage the FDA to ban all antibacterials in those other 700 products ? The average American urinates Triclosan, a common antibacterial in these products.

Glcophosate, plus it’s surfactants are killing our harmonious bacteria, while not harming our bad bacteria. Please, encourage the EPA to understand that just because we humans do not have a shikimate pathway, our beneficial microbes that we live with, do. Roundup, with it’s surfactants, is an epic mistake.

Bacteria are bacteria. The emulsifiers in processed foods cause inflammation in the mouse model. Will you lend your efforts to research into whether these emulsifiers harm our harmonious bacteria, or not ? We need to solve this in 2017. If, these emulsifiers are the cause of leaky gut, it is an epic mistake, leading to a host of auto-immune diseases. We need to solve this.

We know that leaky gut, or damage to the intestinal epithelium, is associated/correlated with damage to the gut microbiome. How about the blood-brain barrier ? Is the same damage to the gut microbiome associated with damage to the blood-brain barrier, (bacteria travel in our blood) and hence, is this a connection with Autism ? I have read where Autism symptoms have been reversed, to some degree, by an FMT. We also know that many Autistic patients have gastrointestinal symptoms/issues.

Since you and I are mostly bacteria, (bacteria cells outnumber human cells by 1.3 to 1) it doesn’t make sense to drink a product that kills bacteria, on a daily basis. We even bathe in it. It’s Chlorine, and it kills bacteria. Since we have 600 to 800 species of bacteria in our oral microbiome alone, plus the many other, mostly helpful, species of our other microbiomes, it doesn’t make sense to expose ourselves to a product that kills bacteria. Will you help to correct this mistake please ?

Mouthwash kills bacteria. Same analysis as above………..

It’s time we look at every single product, food additive, chemical, pesticide, herbicide, etc. and ask, “Is this harmful to my beneficial bacteria ?” Don’t you agree ?

Sure, we can study the microbiome for the next 25 years, but………… if we fail to stop the harm that we are doing now, we perpetuate the problem. Please, help.

I understand you’re an investigator and not a clinician. However, the research is the important part! According to your research, is there any evidence pointing towards dietary changes affecting the microbiome in a positive way? Or taking various supplements? As you might imagine as a clinician I advise patients to try particular dietary protocols that include eliminating all grains and pseudo-grains, starchy vegetables, dairy and sugar, sometimes fruit as well. Does your research suggest that such protocols could provide some benefit for the microbiota that we want to thrive?

So — my research recently has been on (1) seagrass (2) corn (3) birds (4) flies (5) Antarctica (6) marine sediment (7) and more “environmental” projects. I just do very little on humans or even mammals these days. So my research is not really relevant here either. I follow the field and the literature reasonably closely but not enough to make any such specific recommendations. I can tell you that seagrasses really seem to need certain types of sulfur metabolizing microbes … but I can’t really say much about what humans need.